The smart thing, financially, to do is buy a complete new bike (especially going from a Sora 8 speed to a 105 or better setup where you can't really even think about upgrading one part at a time).
I think you've figured that out.
So the question becomes what to do about the Avail and what to do about a commuter.
The two solutions I can see:
1) Keep the Avail because you like it and are attached to it. Invest in some good locks and a rack and use it for commuting. I have done just this with an OCR3 (which is, essentially an Avail) and have had no problems, even in reasonably high crime areas (commuted for 1.5 yrs in San Jose/San Fran Cali and going on 2yrs commuting to CU Boulder in CO).
2) Sell it and buy a junker for a commuter. And I do mean a junker. Get on craigslist or go to a bikeswap and get something for LESS THAN $150 to commute on. There's really no theft deterrent benefit of selling a $600-700 bike and replacing it with a $500 bike.
I'd go with option 1 (I have, I'm biased). Here's why. 1) you're attached 2) you won't get as much for the Avail as you'll think you should (due to exactly the reasons you're contemplating buying a whole new bike now. They get outgrown fast and are limited (8 speed drivetrain) so it won't compete with a 105 or Ultegra 10 speed bike that's maybe a year or two older at the same price)